issue contents

Journal logoBIOLOGICAL
ISSN: 1399-0047

January 2007 issue

Crystallography of complexes

Proceedings of the CCP4 study weekend

Highlighted illustration

Cover illustration: Nuclear receptor 1 with bound natural ligand (p. 72).

research papers

Acta Cryst. (2007). D63, 1-8
doi: 10.1107/S090744490603575X
link to html
X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein–protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts.

Acta Cryst. (2007). D63, 9-16
doi: 10.1107/S0907444906047330
link to html
The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques.

Acta Cryst. (2007). D63, 17-25
doi: 10.1107/S0907444906047044
link to html
Structures of protein complexes offer some of the most interesting insights into biological processes. In this article, the methods required to show that the complex observed is the physiological one are investigated.

Acta Cryst. (2007). D63, 26-31
doi: 10.1107/S0907444906046373
link to html
The use of isothermal titration calorimetry (ITC) provides a full thermodynamic characterization of an interaction in one experiment. The determination of the affinity is an important value; however, the additional layer of information provided by the change in enthalpy and entropy can help in understanding the biology. This is demonstrated with respect to tyrosine kinase-mediated signal transduction.

Acta Cryst. (2007). D63, 32-41
doi: 10.1107/S0907444906045975
link to html
Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described.

Acta Cryst. (2007). D63, 42-49
doi: 10.1107/S0907444906041059
link to html
A method for detecting structural homologs of components in an intermediate resolution cryo-EM map and their spatial configuration is presented.

Acta Cryst. (2007). D63, 50-57
doi: 10.1107/S0907444906046762
link to html
This paper presents a survey of techniques that explore the surface properties of protein:protein interfaces so as to inform the prediction of probable sites of protein:protein interaction on newly determined protein structures.

Acta Cryst. (2007). D63, 58-61
doi: 10.1107/S090744490604604X
link to html
A brief summary of the types of restraint defined in refinement dictionaries.

Acta Cryst. (2007). D63, 62-71
doi: 10.1107/S0907444906051869
link to html
This paper highlights some of the problems that can arise when attempting to obtain crystal structures of small molecule–protein complexes and how biophysical methods can be used to define and overcome these problems. Many of the techniques mentioned are also applicable to the study of protein–protein complexes and mode-of-action analysis.

Acta Cryst. (2007). D63, 72-79
doi: 10.1107/S0907444906047020
link to html
Methods presented for growing protein–ligand complexes fall into the categories of co-expression of the protein with the ligands of interest, use of the ligands during protein purification, cocrystallization and soaking the ligands into existing crystals.

Acta Cryst. (2007). D63, 80-93
doi: 10.1107/S0907444906047287
link to html
A case study showing how the determination of multiple cocrystal structures of the protein tyrosine kinase c-Abl was used to support drug discovery, resulting in a compound effective in the treatment of chronic myelogenous leukaemia.

link to html
Methods and resources for obtaining chemically plausible starting models and restraint sets for refinement of ligand complexes are described and some of the potential pitfalls are discussed.

link to html
An automated ligand-fitting procedure is applied to (FoFc)exp(iφc) difference density for 200 commonly found ligands from macromolecular structures in the Protein Data Bank to identify ligands from density maps.

link to html
The performance of the ligand-building module of the ARP/wARP software suite is assessed through a large-scale test on known protein–ligand complexes. The results provide a detailed benchmark and guidelines for future improvements.
Follow Acta Cryst. D
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds